Predicted ocean acidification and warming are likely to have major implications for marine organisms, especially marine calcifiers. However, little information is available on the response of marine benthic communities as a whole to predicted changes. Here, we experimentally examined the combined effects of temperature and partial pressure of carbon dioxide (pCO2) increases on the response of maerl bed assemblages, composed of living and dead thalli of the free-living coralline alga Lithothamnion corallioides, epiphytic fleshy algae, and grazer species. Two 3-month experiments were performed in the winter and summer seasons in mesocosms with four different combinations of pCO2 (ambient and high pCO2) and temperature (ambient and +3 °C). The response of maerl assemblages was assessed using metabolic measurements at the species and assemblage scales. This study suggests that seasonal variability represents an important driver influencing the magnitude and the direction of species and community response to climate change. Gross primary production and respiration of assemblages was enhanced by high pCO2 conditions in the summer. This positive effect was attributed to the increase in epiphyte biomass, which benefited from higher CO2 concentrations for growth and primary production. Conversely, high pCO2 drastically decreased the calcification rates in assemblages. This response can be attributed to the decline in calcification rates of living L. corallioides due to acidification and increased dissolution of dead L. corallioides. Future changes in pCO2 and temperature are likely to promote the development of non-calcifying algae to the detriment of the engineer species L. corallioides. The development of fleshy algae may be modulated by the ability of grazers to regulate epiphyte growth. However, our results suggest that predicted changes will negatively affect the metabolism of grazers and potentially their ability to control epiphyte abundance. We show here that the effects of pCO2 and temperature on maerl bed communities were weakened when these factors were combined. This underlines the importance of examining multi-factorial approaches and community-level processes, which integrate species interactions, to better understand the impact of global change on marine ecosystems.